No, I don't think the Uighurs have ever been an existential threat to China. I think what they do see, though, is that Uighur autonomy and Uighur society, as it was, was preventing open access to markets and to the natural resources of the region. That was part of the reason they wanted to re-engineer them and, through that process, remove them from their land to make it available for Han settlers and Han companies to exploit and to extract resources. That was how I understood what was happening.
China did see them to some extent as a security threat, the primary security threat that China has. My understanding, based on all the evidence I have seen, is that this was a gross exaggeration.